Cause and Effect
by Kunoichi Umi
Summary: Response to a Prompt on TFBunnyFarm on LJ: In which Sam is the Doctor under the Chameleon Arch. Time is not exactly a straight progression of cause and effect. It's more of a big ball of Timey Whimey, Wibbly Wobbly... Stuff... Non-Linear one-shots.
1. Changes

Title: Cause and Effect

Disclaimer: I neither own Doctor Who nor Transformers. Both belong to all respective creators, producers, and distributors. I make no money from this work of fiction.

Rating: PG-13

Characters: Sam, 11th

Summary: Time is not a smooth Progression of Cause and Effect. It is actually a great big ball of Timey Whimey, Wibbly Wobbly... Stuff...

Note: Response to TFBunnyFarm on LJ: In Which Sam is the Doctor Under the influence of the Chameleon Arch.

Sam remembers Ratchet telling him how devastated Bumblebee had been when the concussion wave from Megatron's Fusion Cannon catapulted him into the air and the damage to his internals and the impact killed him. He remembers how before jerking wholly back into the land of the living, how he spoke to the Dynasty of Primes in that place of towering silica structures that hummed softly as the ground thrummed under his feet and the air smelled of ozone and warm metal and fresh turned earth and the pale mist was dry and cool against his skin.

He remembers drifting in warm darkness as his skin tingled and his limbs surged with strength and vitality, how he could smell hot sand and gunpowder and scorched ozone from the firing of energy weapons and the sickly sweet and sour of human sweat (Disgusting! How had he never noticed it before?), mingled with the copper tang of blood (His blood) and salt from tears (Who was crying?), and the air was filled with the thick, cloying sweetness of death (When had this started?).

Slowly, awareness seeped back, the tiny, tiny grains of sand beneath him, the shifting of air from natural winds, the helicopters or the movement of human and autobot alike, the heat that rose from the sand, the rumbling of the earth as tons and tons of sand shifted. He could feel it, a faint tha-thump of his heart, and a faint echo somewhere in the back of his mind, thump-thump-thump-thump, a twin heart beat that was missing,and that was wrong-wrong-wrong, but at the same time, right. His entire body was being tugged, a faint but powerful pulling, which he somehow knew was the planet moving, spinning beneath his body as it hurtled through empty space, round and round the Sun at thousands of kilometers per second, and he and all other life were there, clinging to the skin of this tiny little blue planet, and if that force, even for a single moment let go...

The simple thought of the consequences, a series of effects after effect after effect with branches of possible effects followed by possible effect, all preceded by causes and effects that had already passed, frightened him. He lunged for the tiny pinprick of light in the distance...

And jerked awake in the desert in the ruins of a village, the merciless Egyptian sun beating down upon them as gunshots echoed around them and explosives were launched and detonated. Warm arms were cradling his head, he could smell salt and citrus and motor oil, and golden-brown threads shifted around the woman holding him winding around his muzzy consciousness, and all around him, other glowing threads (the personal timelines of the Mechs and Humans on the particular stretch of desert) shifted, stretching into the distance, diverging and converging, and in the cases of the dead or soon to be dead, stopped abruptly.

And that was when he knew that he was no longer entirely human, because the gaping silence in his mind was raw, raw and terrible and just _wrong_and oh! Oh, there were memories that shouldn't be there, memories that, yes, they were his, but at the same time not, because there was an echo of a second heart in his mind, one that was and was not his, and drat it all, how could this have happened? The Chameleon Arch was supposed to have sealed the Time Lord essence in a fob watch, one which was left amongst his personal belongings back in the dormitory in Princeton...

And yet...

And yet here he was, his body and genetics were still intrinsically human, he had no doubt of that, but still, his senses and the information his mind was sorting through... He had memories from every incarnation to this point, though what particularly interested him was the memories from his Tenth incarnation and that brief time toward the end when he'd still had a fully functioning pyscho-kinetic link to his newly created two way Human-Time Lord Biological Metacrisis. Both of them. He remembered through them, the Human Doctor and the Doctor Donna, how it felt to be half human, and through Donna, how it felt to burn. It was eerily similar to when his Ninth Incarnation had drawn the Time Vortex energy out of Rose... And yet this moment, despite having those memories, he wasn't feeling it. He wasn't burning.

Not that he wanted to burn, mind, but considering his situation, it was strange.

Sam blinked and the glow of the threads that represented each individual timeline faded until he could just barely see them. He blinked as a silver glint from the corner of his eye did not fade like the rest, and realized that he was forgetting something. He clambered to his feet and his hand closed around a ribbed and curved metallic object, the Matrix, his most recent memories, _his_ memories, _Sam's_ memories, told him. _A_Matrix, the Time Lord memories insisted, one of a collection of depositories of knowledge, depositories of Gallifreyan knowledge; it's purpose warped and changed over the course of billions of years. But the markers in his human genetic structure left behind by the Chameleon Arch to identify to the fob watch where the essence was to be returned had been read by both AllSpark and Matrix, and both artifacts had begun the process of returning to the use to which they had been meant.

And all it had taken was a Metacrisis to do so.

But there was time to think on the Matrix and the knowledge contained therein later. First, he had a Mech to resurrect.

TBC


	2. First Night

Title: Cause and Effect

Disclaimer: I neither own Doctor Who nor Transformers. Both belong to all respective creators, producers, and distributors. I make no money from this work of fiction.

Characters: Sam, 11th Doctor, 10.5 Doctor

Summary: Non-Linear. The fact that he had all this awareness, all this knowledge while the fob watch containing his Time Lord essence sat in a box amongst his not quite unpacked possessions in Princeton frightened him. Partially because he had no idea how a Chameleon Arch might affect him.

**Chapter 1: First Night**

The conversion had been a hard one. Granted that Sam had been dead in the five minutes during which the conversion had taken place, the waking had been much less pleasant. Every movement had sent fresh bursts of raw, screaming pain through his nerves, though he'd barely felt it, so preoccupied he'd been with sorting out the information bombarding him from his new (old) senses. It had been a shock to one moment be cradled in warmth and insulated from the pain of his injuries, then wake to find himself with a new awareness of his place in time and space, though the awareness was dimmed, a sensation remembered from a different life as a different man, gained from a psycho-kinetic link that no longer existed primarily because the matching biological structure and mind was gone, burned away in the fires of regeneration.

Frankly, the fact that he had all this awareness, all this knowledge while the fob watch containing his Time Lord essence sat in a box amongst his not quite unpacked possessions in Princeton frightened him. Partially because he had no idea how a Chameleon Arch might affect a Metacrisis.

Then there was also his dependence on the sonic screwdriver to contend with. A sonic screwdriver that was in the Tardis, parked in Sir Alistair Gordon Lethbridge-Stewart's garden in the United Kingdom. Granted, he didn't really _need_ the sonic screwdriver, he'd gone through almost seven regenerations without really using the sonic all that much, but in his later years, his Ninth and Tenth, and most recently, his Eleventh had been almost completely dependent on the sonic screwdriver. Not that he was incapable of doing anything without it, it was a case of taking the easy way out. It was quite handy, the sonic, and he'd feel all the better for having it.

It was this which drove him to draw aside Captain Graham at the first opportunity to whisper several codes into his ear before asking him to put in a call for one of his companions, preferably Amy or Rory, as previous companions were likely to get lost in the newly refurbished Time Ship, to go into the Tardis and retrieve his sonic screwdriver. And maybe the mobile that Martha had given to him in his Tenth incarnation. The good Captain, newly transferred from U.N.I.T. into N.E.S.T., was shocked to learn that he was the Doctor, a near legendary figure in the U.N.I.T. archives, the famed (or infamous as the case may be) scientific advisor of U.N.I.T. from the eighties, but quickly overcame his surprise and obediently made the calls. Three days later, the Captain was personally presenting Sam with a package containing both sonic and mobile. The salute that followed left the young man grumbling under his breath to the amusement of the U.N.I.T. affiliated soldiers who had heard a great deal about the Doctor.

Having the sonic screwdriver in his recently acquired dimensionally transcendental pockets lifted one weight off his shoulders but added another. The handiness of the tool meant that he'd kept adding function after function, until the sonic screwdriver could deal with just about anything, with the exception of wood. He'd known he relied too much on the sonic and it was time to break the habit, because feeling naked and uneasy about going only five days without the screwdriver was a major no-no. Having his hands itch for the sonic screwdriver when the situation did not warrant the use of so advanced a piece of technology was unacceptable, and was a habit he'd have to break. And he'd take advantage if his time in Princeton to break the habit.

-

The truth of the matter was, despite being half-human, a Human-Time Lord Meta-crisis took after the Time Lord side more than the Human side, at least, where IQ and extra sensory perception was concerned. The first night after the entire debacle with the Fallen and being chased across the globe by international intelligence agencies, Sam had spent some time in a trance state, sorting through his mind and the knowledge that the Matrix had altered him to contain without burning. That the human part of his new make-up could use that time to rest and recover was only a bonus. Of course, this didn't mean that he did not need to sleep at all, even a Time Lord needed _some_ sleep, though not as much as a Human. It didn't change the fact that he slept twice as much as the average Time Lord, that is to say, an average of eight hours a week, Earth time.

And so it was five days after Egypt, when Sam and Leo had been resettled in their dormitories in Princeton, that Sam finally allowed his mind to rest along with his body.

Sleep came with little difficulty. With the application of the breathing and meditation exercises that all Time Lords were required to master, he'd fallen from the world of the waking into the realm of dreams as seamlessly as each breath he took...

-

_A solitary figure, hooded and cloaked, carried a box through the mausoleum, past shelf after shelf of blankly staring human skulls._

_"Who is that? Who is carrying me? I demand to know!" a voice demanded angrily from the box. "I'm a head. I have rights. I want my doors open this time."_

_The cloaked figure set the box onto a plinth._

_"I demand that my door is open!"_

_The figure slid open the box with a swift gesture to reveal a bald blue head. Wordlessly, the figure turned and walked away._

_"Is it you? It is you isn't it?" the disembodied head asked. The figure paused and slowly shuffled around to partially face the head. "It is you! I can sense it! How did you do it? How could you have possibly escaped!"_

_The figure dropped the cape to reveal a youngish man with floppy brown hair and green eyes clad in a distinctive tweed jacket with a blue bowtie. He turned and smirked at the befuddled head._

_"The Teselecta. The Doctor in a Doctor suit," he sounded unmistakably smug as he strode toward the disembodied head on a plinth. "Time said I had to be on that beach, so I dressed for the occasion. Barely got singed in that boat."_

_"So you're really going to do this? Let them all think you're dead."_

_"It's the only way. Then they can all forget me. I got too big, Dorium, too noisy. It's time to step back in to the shadows."_

_"And Doctor Song? Imprisoned all her days?"_

_"Her days, yes," the Doctor agreed, "As for her nights, well," his lips twitched into a suggestive smile, "that's between her and me, isn't it?"_

_Dorium chuckled. "So many secrets, Doctor, of course, I'll help you keep them."_

_"Well, you're not exactly going anywhere are you?"_

_"But you're a fool nonetheless," Dorium's voice shifted from amused camaraderie to rebuking in seconds, "It's all still waiting for you, The Fields of Trenzalore, the Fall of the Eleventh, and the Question."_

_The Doctor smiled and mock saluted the head in a box, "Goodbye, Dorium." He turned and strode away without looking back._

_"The first question: the question that must never be answered: hidden in plain sight!" Dorium's voice rose as the Doctor got farther and farther away, "The question you've been running from all your life!"_

_That line wiped any hint of geniality from the Doctor's face as he increased his pace slightly._

_"Doctor who?"_

_The Doctor paused in front of his TARDIS and turned to look back, lifting his head slowly._

_"Doctor who?" Dorium called._

_Unseen by the head, a corner of the Doctor's lips lifted in a wry, cold smirk._

_"Doctor WHO!"_

-

The young man jerked awake, sitting up with a gasp. He stared blankly at the poster covered walls in front of him for a moment before turning slightly and taking in the entire dormitory and his roommate curled up under the covers in the bed on the other side of the room. The room was silent but for the ticking of a clock and the soft, whuffling snores of his roommate.

He turned and pulled open a drawer in the bedside table and drew out a small silver pocketwatch engraved in an elaborate pattern and concentric circles. He held it gently in his right hand, gently thumbing the catch, but applying no pressure. He could hear a faint whispering from the watch, and the weight and warmth of ages oozing from the aged metal. The young man known as Samuel James Witwicky twisted in his bed and reached under his pillow to pull out a cylindrical object seemingly made of brass topped by a green bulb in silver brackets. He aimed it at one of the three desktop computers and pressed a button, and the green bulb flashed to life with a low whining buzz, and the computer monitor lit up. He stopped pressing the button, and the light and buzzing ceased, and Sam smiled a slow, secretive smile, one reminiscent of a floppy haired man with a love for tweed a bowties whom many thought to have died not too long ago on the shores of a lake in Utah.

-

TBC.


	3. Bad Night

bTitle:/b Cause and Effect

bDisclaimer:/b I neither own Doctor Who nor Transformers. Both belong to all respective creators, producers, and distributors. I make no money from this work of fiction.

bRating:/b PG-13

bCharacters:/b Sam, 11th Doctor, River Song

bSummary:/b Non-linear. They always leave. Sometimes they go because they have to, sometimes they go because it is no longer fun. In the end, I suppose, they break my hearts.

centerbuChapter 2: Bad Night/u/b/center

He is always alone in the end. It started on Gallifrey when he had still been a child. Eight years old, brought before the Untempered Schism, where he and all his peers learned their true natures. Some were inspired, some ran away, and some went mad. Like Koschei. For the better part of a thousand years, he had thought Koschei's drums were all in his head, just an auditory hallucination. He had believed that if Koschei, clever, skilled, focused, Koschei would only concentrate, the drums would go away.

It didn't work, and the day they graduated and chose their new titles, the day he had left behind Theta Sigma of Lungbarrow to become The Doctor, was also the day Koscheivaridamarille pae Oakdown became The Master. It was the day they stopped being friends and became rivals, and later, enemies.

He remembers the beginning, Theta and Koschei spending entire days running across the fields of red grass stretching past the sides of Mount Perdition, hollering their dreams to the orange sky as twin suns shone down on them. Then came the days when The Master would leave him a Clue, wait for him to find it, make his move, then counter it, a stately game of chess. A Gentleman's Battle, a struggle between two Time Lords who mirrored each other exactly. Later it got darker, uglier, it became less civilized and it was a struggle of figure out what he's doing and hit him before he hits you and ensure that he doesn't get to recover between hits. Until the end. The End of Time, when he'd destroyed the Time Lords for the second time, and in that moment, it had been their childhood again, Theta and Koschei, two troublemakers amidst the traditions of Time Lord Society, and the Time Lock was restored. Koschei was gone, living only in his memories, and The Master, created by the Time Lords in their push for power, just one more regret in a long line of regrets.

He remembers the early days: Susan, Barbara and Ian, Jamie and Zoe, The Brigadier, Jo and Sergeant Benton and Mike Yates. Oh, then the middle days, where he became older and wiser: Sarah Jane, Romana and Adric, Tegan and Nyssa. And then the days where he had been disturbed, because there was a storm coming, a big one, one he'd felt regenerations before it came: Peri, Ace, Grace. And the days after, those bright, ended too soon days when he'd been a wreck: Rose and Jack and Mickey, Martha and Donna and Astrid and Wilfred, Amy and Rory and River... Oh, but they had been so many, and many more in between, these bright, beautiful, magnificent people... And Tegan and Sarah Jane and Rory were right in the end. He took them, these sweet, innocent, brilliant people, and he changed them. Some became soldiers, some died, some were lost to space and time, some went home to muddle through as best as they could. They left because there was something better out there, an even greater adventure than the one he could ever provide, because frankly, lets face it, running through corridors gets old after a while, and even the Doctor wishes for the early days with Susan and Barbara and Ian and Sarah Jane where running for one's life was not the norm, no matter how brilliant it had been in the end, running with Tegan and Rose and Martha and Donna and Amy and River.

Sam stood beside the rusted remains of a strong Mech, green eyes fixed on the head, which had fallen off and rolled away at the last moment of his life. He'd run with Ironhide only twice, both times, he had been the one being protected, a change from the norm, considering that he'd always been the one to protect his companions as best he could. It seemed that even when he was the companion instead of the guide, his friends still left him.

Because Ironhide was not the only casualty. They had lost Jazz in Mission City. In Egypt they'd lost Arcee and Jetfire. And most recently, in Chicago they had lost Que and Dino and Skids and Mudflap and Brains and Wheelie. Good friends all, some he knew well, some he didn't, and most of all, some he didn't know as well as he would have liked, and some he liked less than they deserved.

There was a flash and the scorched smell of ozone behind him.

"Hello, Sweetie," a sultry voice purred.

He didn't need to turn and look to see the curly haired woman behind him, smiling secretively at his back.

"River," he acknowledged her presence with that one word, this woman, his wife, who had overseen the preparations for his life once he'd gone under the Chameleon Arch.

"They were good people," River said, walking to stand beside her husband, "and they were your friends. They wouldn't want you to mourn."

"They all leave me in the end," Sam said softly, "Even when I'm the Companion instead of the other way around."

"You, Doctor," River said sternly, "You leave them also. You pluck these people out of their comfortable, ordered lives, throw them into chaos, show them the stars and the wonderful things about the universe, then dump them back home to muddle through as best as they can. You run away with your Tardis, but they can't. Yes, they leave you, but you leave them just the same."

"Yeah," Sam agreed reluctantly, "I do don't I?"

River surveyed the young/old man beside her briefly before breaking out in a grin.

"Come on, Doctor," she said gaily, looping her arm around his, "There's a festival taking place on Danzilar Twelve in the Fifty Second Century. You owe me a Birthday Party, remember?"

Sam straightened his back and grinned just as brightly, "Off we go then!" He pulled out the Sonic Screwdriver and buzzed it over River's Vortex Manipulator, and the two of them vanished in a flash of light, leaving behind a wisp of smoke and the scent of scorched ozone.

A yellow Camaro with black racing stripes watched the two vanish, and a low whine of static, borne of fear and confusion issued from the radio.

TBC


	4. Long Night

Title: Cause and Effect  
>Disclaimer: I neither own Doctor Who nor Transformers. Both belong to all respective creators, producers, and distributors. I make no money from this work of fiction.<br>Rating: PG-13  
>Characters: Sam, Bumblebee, Optimus, , 11th Doctor, River Song<br>Summary: Non-linear. Sometimes he wonders if the modern-day UNIT has lost their minds, because they call him to investigate cases like missing people, giant spectral hounds, and missing rabbits. Honestly, this is not an episode of a BBC pilot that won't be aired for another two years!

**Chapter 3: Long Night**

The Autobots don't entirely understand the changes in Sam after Egypt. The boy had distanced himself further from Bumblebee and one would think dying to revive Optimus would bring them closer than ever. But it doesn't. What DOES happen is that Sam's relationship with NEST changes entirely.

Where once, Sam eagerly made the trip NEST HQ at Diego Garcia as often as the Autobots, Lennox and General Morshower could contrive for his holidays, now he would rather go to a military base on the outskirts of Sacramento, one affiliated with UNIT and not only did UNIT not stop him, they practically slavered over the boy. In the time when Sam was at Princeton, he would go to a base just outside the city. In this particular case, UNIT had seen fit to ask for Sam, and Sam agreed and they'd gotten onto a Military Cargo plane, and were shipped off to the U.K.. As was the case at the UNIT base in Sacramento and Princeton, Bumblebee was allowed onto the Base, but he wasn't allowed iin/i it, and Sam didn't argue.

In fact, he'd shrugged, and patted his hood and said in an amused and entirely unsurprised tone, "UNIT knows exactly what you are, Bumblebee. And knowing what UNIT exists for, it's a miracle they let you onto the base at all, rather than shooting you on sight."

Bumblebee had chirped in alarm, and Sam shrugged again, "They do that sometimes, shoot things even though they know the bullets won't work." He smiled affectionately at the corporal (who kept shooting Bumblebee wary looks) standing beside a military jeep, the door still ajar from when he'd opened it as invitation to Sam, "They're pigheaded that way. But good people. I like UNIT."

Bumblebee noted how every human in hearing range straightened at that, and Sam chuckled. "Don't worry," he patted Bumblebee's roof affectionately, "I brought you in, so you're not in any danger." He paused and glanced over at several soldiers busily painting the outside of a warehouse and amended quickly, "No permanent danger at least. Your pride and paint job may suffer, but it won't be all that bad. So sit tight, buddy, I'll be back before you know it."

Bumblebee watches as Sam climbs into the jeep and Corporal Ryans closed the door. The Corporal moved to climb into the back of the Jeep and murmured quietly, "A Camaro, sir? Parked next to your Bessie and the same shade of yellow? No one has the bollocks to prank _you_, Sir."

Sam threw his head back and laughed as the driver of the Jeep stepped on the accelerator and drove away, leaving Bumblebee parked behind a warehouse next to an old fashioned yellow roadster.

Sam knows that it was a bad idea using Bumblebee as a conveyance when he was needed at UNIT HQ in Sacramento or Princeton. He knew it and did it anyway, because college was iboring/i and ever since he'd gotten back from Egypt, his mind was a Time Lord mind, and it was at all times whizzing about at a hundred thoughts per chronon, which added up to ten thousand thoughts per nanosecond, and ramped it up to a hundred million thoughts a second. All of this meant that if he didn't find some sort of entertainment that had nothing to do with the ridiculously simple so-called higher education that humans believed was advanced, he would go mad. He'd become like the Master before Gallifrey was Time-Locked the second time, and go on a wild conquering and murdering spree. Never mind the conquering/murdering spree, The Moment was still in his Tardis, and since her last reconfiguration, it had become integrated into her systems, which meant there was a good chance that if he snapped, he might go off and Time-Lock a bunch of innocent worlds just for the hell of it. It was not a pretty prospect, and the thought of it left Sam shivering and feeling dirty.

So he sought out UNIT.

And thank goodness for Captain Thomas Graham, because he'd warned UNIT that the Doctor was aware although he'd chosen to (mostly) retain his cover. As for the leaders of UNIT? The commanders of UNIT had no qualms taking advantage of the thoroughly bored genius Time Lord who was housed nearby.

For Sam, it was a godsend, because for one, he was not quite as bored anymore, especially as it seemed that Earth got invaded practically every other week. The only downside was that the invasions tended to be minor and relatively easy to stop, and seemed mostly centered in London or Cardiff, but hey, a distraction was a distraction, and since he no longer had access to his time ship, the Tardis being across the pond parked in Alistair Gordon Lethbridge-Stewart's garden and all, he could no longer watch BBC shows that wouldn't be aired just yet. Which was a shame because the Doctor's favorite documentary about Gallifrey (He'd particularly enjoyed poking fun at it and River sometimes joined in the fun by writing scathing letters about the mistakes in the rendition of culture and fashion.) wouldn't be aired by the BBC for another nineteen hundred years.

Of course, boredom was not the only reason why Sam fled the presence of the Autobots of late. It was not widely advertised, but on Gallifrey, having technology that responded to psychic prompts was a way of life. It made life quite simple, and frankly, the Time Lords were often lazy, and so being able to turn on a light with a telepathic nudge was convenient and took little effort. Even the sonic screwdriver had what Rory once very aptly called the "Point and think function" installed.

Unfortunately, it meant that technology based off Time Lord technology would have these inbuilt prompts as well. Which meant that the Autobots (Optimus in particular was vulnerable because of his possession of a Matrix) could, without knowing why they did it, unleash their weapons if Sam was annoyed while touching them and imagining the gory demise of the irritant. Worse, because they were sentient, such an intrusion, unconscious or otherwise would eventually be detected, and how long would it be before it was Sam himself who was the threat? No the less contact Sam had with Autobots, the better. It hardly mattered that Optimus, because of the Matrix, could sense his mental touch, because Optimus thought he knew the function of the Matrix, but he really didn't. No, Optimus Prime thought he could sense Sam because he'd activated the Matrix, which meant the Matrix had formed a Brother-Bond between them, making Sam the first ever Human Prime.

Wrong.

Very Wrong.

Very, _very_ wrong.

Yes, the Matrix had a quantum bond with all its counterparts, which was partially how Optimus could feel Sam's mental footprint, but the quantum bond was formed because at some point in between being launched off Gallifrey before the Final Sanction was activated and the Moment Time-Locking the Time War, and landing in what would eventually be Cybertron, the Matrix had shattered into thirteen pieces before being scattered across Time and Space. As far as getting information out of the Matrix was concerned, Sam would have to collect all thirteen Matrix segments and reassemble them in order to have a complete compendium to draw from, and frankly, he was _not_ in the mood to go on an epic quest across Time and Space to find the missing parts of the Matrix. He'd had enough of Epic Quests since gathering the Key of Time with Romana in his Fourth Incarnation, say nothing of the adventure with the Pandorica or even the fiasco at Demon's Run, thank you very much.

This meant he had only two other options, the first of which was to consult the remnants of the Cube, which he's tried. Unfortunately, the Cube being what it was, a Prototype of the Eye of Harmony, it wasn't exactly sentient. In fact, the Cube hadn't gained sentience until the arrival of the Matrix led to the Dynasty of Primes being sparked. This meant any information contained within the Cube, despite being Gallifreyan in origin, was primarily concerned with the history of Cybertron. Well, there was always the second option, the Tardis Library. The Tardis Library in the Tardis which was parked in Sir Alistair Gordon Lethbridge-Stewart's garden.

Hence why he was on a UNIT Base in Britain today.

Well, partially.

Just last week, Graham had handed him a dossier, and asked him to read it while on live feed with UNIT and the retired Brigadier. Apparently there had been strange reports up and down the Dartmoor, in the area known as Baskerville. Several people had gone missing, and to top it all off, there was an escaped rabbit. An escaped, glowing rabbit. No, seriously. Sam had raised an eyebrow at this and asked quite bluntly if the current commanders of UNIT had thought they were being funny, because frankly, this was real life and _not_ an episode of a wildly popular BBC pilot that would not be aired for another two years and by the way, hadn't he _already_ dealt with a similar investigation back in the _seventies_?

The only response he'd gotten from UNIT was confused and embarrassed shifting and the Brigadier responding with an irate, "All the more reason for you to come up and investigate, Doctor! Now get on that blasted plane!"

And so here he was, tromping through the Dartmoor in the middle of the night with six UNIT soldiers armed to the teeth with only torches to light the way. Sam sighed irritably. The more things change, the more things stayed the same. This was going to be a very long night.

TBC


	5. Strange Day

**Title:** Cause and Effect**  
>Disclaimer:<strong> I neither own Doctor Who nor Transformers. Both belong to all respective creators, producers, and distributors. I make no money from this work of fiction.  
><strong>Rating:<strong> PG-13  
><strong>Characters:<strong> Sam, Bumblebee, Captain Graham, UNIT  
><strong>Summary:<strong> "For six months, Sam went through the process of cutting ties with the Autobots, or at least that was what it looked like to Bumblebee. He never realized that it was the Autobots themselves that was causing Sam to withdraw from them, not because Sam was bored of them or because he no longer cared, but because Sam cared far too much…

Bumblebee thought everything would change after Egypt. He thought that he and Sam would become closer than ever, that Sam would have learned that he needed Bumblebee, and since the Matrix had glowed in his hands, Bumblebee was sure that Sam would be spending a great deal more time at Diego Garcia with NEST.

He was right in that everything changed, because everything _did_ change. Sam grew up in the few days that they had been searching for the Matrix, and his brief death in Giza matured him even more. Sam who was intelligent from the start, started thinking before he acted or spoke, and became exceedingly careful in choosing his words, and perhaps the Matrix changed his brain or something because he became, in Leo's words, scary smart. But that was where the trouble began. Bumblebee quickly learned that he was wrong in thinking that he and Sam would be closer than ever before, and he was even more wrong in thinking that Sam would be spending more time at NEST HQ, because about twelve weeks after Egypt, when the Term was finished, Sam got permission to stay with the Autobots at Diego Garcia. It was to be the last visit for a very long time.

For six months, Sam went through the process of cutting ties with the Autobots, or at least that was what it looked like to Bumblebee. He never realized that it was the Autobots themselves that was causing Sam to withdraw from them, not because Sam was bored of them or because he no longer cared, but because Sam cared far too much. It would be at least four years before Bumblebee or the majority of NEST would realize why Sam did the things he did. Until then, Bumblebee would watch from a distance as Sam grew up and grew out of his dependance on the Autobots, because try as he might, Sam kept him at arms length, and Bumblebee found himself becoming less of a Guardian and more of a means of conveyance for Sam to get from point A to point B.

Things only came to a head one day when Sam was in Diego Garcia chatting with Wheeljack and Que (Brothers, the two of them, and no matter the similarities between them appearance wise, Wheeljack was the one who had the emoting head fins which Sam fanboyed over,_"Look at that, Bumblebee! Isn't it gorgeous? Absolutely Brilliant! Fantastic even!"_ much to the amusement of many a 'bot.) and actually making a point and keeping up (To the gleeful surprise of the inventors and to the consternation of Ratchet, _"If that boy starts blowing things up because of your influence, Wheeljack!"_) in the common area when Captain Thomas Graham, with affiliations with UNIT, walked in with several envelopes stuffed with manila files full of papers and photographs, which he plunked down in front of Sam.

Sam promptly broke off the conversation and dove into the papers eagerly, though it only took flipping through the first two files before he glowered at Graham, "Is this it? Autons and Axons and a stray Wycoxx in Cardiff? Boring!"

The last word was shouted at the top of his lungs, followed by a long rant about stupidly not resigning properly and a Nestene Tulip infestation and the reasons for Wycoxx to be present on Earth instead of their home planet which was not even in the same galactic vector as the human home world, all the while, gesturing wildly with his hands like some sort of demented bird and pacing the entire circuit of the very large room meant to accommodate the Autobots in both forms. Autobots who stared at Sam in confusion, as he was acting quite out of character and how did he know some of these things?

Captain Graham, on the other hand, merely rolled his eyes and muttered something about, "Exactly the same as the file said."

Which had Sam spinning around and shouting, "That's it! Oh, Graham, you are brilliant!" he got right in Graham's face and lowered his voice back to normal volume, though he didn't stop his enthusiastic gushing, "UNIT has been handling this the entire time, so since there never was a proper resignation, we can just pop right back in! Quid pro Quo, just like the old days! Won't the Brigadier be pleased? And Sarah Jane! Oh, and Captain Erisa Magambo, I liked her. Interesting woman. And Colonel Alan Mace. Good man, Colonel Mace, but don't tell him I said that. He hasn't met me yet." Here he paused and frowned and turned to Graham and asked, "Speaking of whom, how many vehicles in NEST have ATMOS installed? Never mind, remove all of them. Use the official Secrets Act if you have to, and tell them UNIT's Scientific Advisor highly recommends doing so. ATMOS kills."

Graham paled and saluted and rushed out of the hanger. Sam swept up the papers and left the hanger, muttering in an incomprehensible language under his breath all the while.

One week, later, all the ATMOS were removed from NEST vehicles, and none too soon, because three weeks later, ATMOS all around the world started releasing noxious fumes.

It was only the first sign of how Sam's relationship with the Autobots would change.

~*~

TBC


	6. Hypothetical

**Title:** Cause and Effect**  
>Disclaimer:<strong> I neither own Doctor Who nor Transformers. Both belong to all respective creators, producers, and distributors. I make no money from this work of fiction.  
><strong>Rating:<strong> PG-13  
><strong>Characters:<strong> Sam, Carly, Brains, Captain Graham, 11th Doctor  
><strong>Summary:<strong> "Some things simply did not bear thinking about…"

Chapter 5: Hypothetical

A week after the Dartmoor investigation, centered around a genetically engineered escaped rabbit of all things, Sam made a trip to pick up the Tardis. While there, he encountered Carly Spencer, who, as far as Sam could tell, was a heavy point in Space and Time. Why else would she had a laptop that was a Cybertronian Sparkling? It was suspicious to have such a convenient meeting with someone who also had possession of so precious a-commodity for lack of a better term, in a coffee shop seven blocks away from where the Tardis was parked?

So he did what he always did. Ignoring all convention and common sense, he swooped in and swept Carly off her feet with the intention of observing and analyzing her until he knew exactly what sort of trap had been set for him and how he could best counter said trap. In other words, the Doctor took her with him.

The Tardis, contrary as ever, took off the instant Sam, Graham, and Carly had set foot inside. Carly panicked. Graham clung to a railing for dear life. And Sam? He dashed around the console, flipping switches, turning dials, throwing levers, and pushing buttons, muttering half-hearted imprecations about temperamental Time Ships under his breath all the while.

They found themselves on Rudistal Prime in the Twenty-Ninth Century. Or to be more specific, they found themselves in a University.

A flyer about a lecture on morals and war in the East Tower was posted right at eye level, and was the first thing any of them saw when they left the Tardis. Sam, perhaps taking that as a hint, insisted that they attend. And so they did. And Sam had a blast. Right up until the question was asked.

If the Sontarans ever met the Cybertronians, who would win?

Graham was concerned when he noticed Sam turn ashen. Carly was just confused. Sam promptly grabbed both Graham and Carly by the collar and hauled them out of the auditorium and back to the Tardis. He slammed the doors shut and leapt onto the console and began madly pressing buttons.

When they landed in the foyer of UNIT HQ in London, and Carly was registered into the system as the Doctor's newest Companion and was given clearance, a Code 9, Graham asked Sam the question.

"I have no idea," Sam shrugged, "Frankly though? It's a miracle that the Sontarans haven't attacked the Cybertronians to find out yet. And If you don't mind, I'd like to keep it that way."

It was more of an evasion than an answer, but honestly, the answer to that particular question was so scary, even the Doctor didn't want to think about it.

Because really, if a war ever took place between the Sontarans and the Cybertronians, they would be lucky if there was a universe left over in the end.

~*~

TBC


	7. Cost

**Title:** Cause and Effect**  
>Disclaimer:<strong> I neither own Doctor Who nor Transformers. Both belong to all respective creators, producers, and distributors. I make no money from this work of fiction.  
><strong>Rating:<strong> PG-13  
><strong>Characters:<strong> Sam, Sentinel Prime, Tardis, 11th Doctor  
><strong>Summary:<strong> By the 51st Century, Humans are the most prolific and widespread species in the universe while Cybertronians number only in the tens of thousands, and by the End of the Universe, there are still several billion humans running around while there is not even a memory of the Cybertronians….  
><strong><span>Important Note:<span>** This installment is from the TARDIS POV.

Chapter 6: Cost

He's gone by many names, My Thief. Theta Sigma. Father. Brother. Husband. Grandfather. Professor. Friend. Protector. Oncoming Storm. Love. John Smith. Acquaintance. Destroyer of Worlds. Murderer. Killer of His Own Kind. Sweetheart. Traveller. Lately he goes by the name of Sam, Samuel James Witwicky. But he is best known as The Doctor.

The Doctor has been around for a very long time. Well, not as long as me, because I was a museum piece by the time he was born. So, he hasn't been around all that long, existence-wise, but from his linear perspective, and the perspective of those ignorant of the intricacies of Time-Travel, he's been around for a very, very long time. What? No matter what he told Rose, Martha, Donna, Amy or Rory, he knows his age. When he was younger, before the war, he would tell his companions his true age without hesitation, but now he's getting old, and he can't tell the truth any more. He has to lie, because he's getting younger as he gets older. When asked for his age, My Thief chose a nice round number that would impress, but not intimidate, and Counted from there. And then he carefully crafted a mask that would guide each companion to subconsciously forget that he was older than their civilization and that his civilization was old when Earth was still little more than a cloud of dust and rock and ice.

What? You didn't honestly think that he really was that silly and absentminded? No, he remembers everything he sees and does and says. He knows exactly where he left that hat, that screwdriver, that mug, that spanner, clamp, glove, mallet, pencil, knife, tweezer, etc.

He's good at acting, My Thief, he has to be. He suffers so much, looses so many people, and all I can do is take him from one heartsbreak to the next. So when he decided to stop running for a while, just slow down and remember that he's not a God or all knowing, slow down and remember that he's mortal, I did what I could. Which is actually very little. I'm a sentient Blue Box that traverses Time and Space. Once my Thief and his Companions leave my confines, I can't protect them because all I can do when they are outside of me is sit around, you know.

It's very annoying. Especially when they run up to me, throw my doors open, dive inside and slam my doors shut, and my outer shell is peppered with energy blasts or kinetic projectiles, or a propellant fueled explosion, and in one case, thrown out of a nice pressurized cupboard into cold, empty space. I _do_ remember that arrow sticking out of my door you know. Moving through the Time Vortex at high speeds with a sharp bit of wood embedded in me is not fun at all if anyone is curious. _And_ he leaves the breaks on! Do you have any idea how hard it is to fly when the brakes are on?!

... But I digress.

Most people don't know it, but there is a recall function installed on me. It used to be used to call me back to Gallifrey, but when Gallifrey burned, My Thief fixed it so all he has to do is use Emergency Setting Two on his Sonic Screwdriver to call me to him. He rarely does. The closest he ever came to using the Emergency Recall Function was when he first met Donna and they had to vacate the area. Why am I bringing this up? It's not relevant to this story is it? Just... Keep this in mind for later. I promise you it will be important.

So where was I? Ah, yes. My Thief. He's called Sam now. Samuel James Witwicky, and sometimes I don't know what to do with him, he gets into so much trouble. Even with his biology rewritten, he attracts trouble. But that's one of his charms, I suppose, and this penchant for trouble is partially what makes him so well known, that and his minor hero complex. But he doesn't look for trouble, he's easily depressed, but not suicidal. These things just happen.

Which is why when My Thief hears Sentinel Prime intone, quite solemnly, "The needs of the Many outweigh the Needs of the Few," he gets himself into trouble. Because he simply can't help but laugh.

He can't be blamed, really. Honestly, what was the population of Cybertron before the War? Seventy Million? What about now? Forty-five Thousand. By the 51st Century? About 23 Hundred. The End of the Universe? Maybe a rusted shell or three that no one knows the origin of and gets scavenged for parts to build a ship to take humanity to Utopia. And what's the population of Humanity now? Seven Billion? In the 51st Century? 67 Quadrillion? The End of the Universe? Seven Billion give or take a thousand?

Oh, Sentinel gets all offended, so My Thief does the smart thing. He's still laughing, but he pulls out his sonic screwdriver and hits Emergency Function 2. My extrapolator shielding keeps us from being blown to itty bitty bits, and I dematerialize into the Time Vortex to keep the unstable Prime from stepping on us.

Honestly, even half-human, he gets into so much trouble.

But that's just how he is, My Thief.

~*~

TBC


	8. Exile

**Title:** Cause and Effect

**Disclaimer:** I neither own Doctor Who nor Transformers. Both belong to all respective creators, producers, and distributors. I make no money from this work of fiction.

**Rating:** PG-13

**Characters:** Sam, Charlotte Mearing

**Summary:** It will affect your standing with everyone involved, however, I need you to ban me from NEST.

Chapter 7: Exile

She knew from the reports the importance of the civilian codenamed The Boy was to the Autobots. It was just so obvious. Within a week of making first contact, The Boy had been assigned a Guardian, the yellow Camaro, what was his name? Ah, yes. Bumblebee. All one had to do was mention The Boy in passing, and immediately, the attention of every Autobot in hearing range was fixed on you.

It was an attentiveness that bordered on obsession, and Mearing couldn't help but be alarmed. She realized a few days later that almost the entirety of NEST treated The Boy as if he were some fragile thing, breakable, precious, without peer or value. And The Boy _hated_ it. He took refuge with the British contingent of NEST, but even so, a good deal of them treated him as if they were in the presence of a living legend. It turned out that those members of the British contingent had affiliations with UNIT, and were aware of The Boy's connection with the famed Scientific Advisor known simply as The Doctor. She frowned at the files on her desk. All that constant attention and coddling simply could not be good for the young man's mentality.

There was a knock on her door, and she glanced up and smirked to find The Boy kicking the door shut behind him, two cups of coffee in his hands. Speak of the Devil.

"Got tired of the smothering, I see."

"You have no idea." He rolled his eyes and handed her a cup before taking a seat in front of her. "I need you to do something for me before I go insane."

She took a sip of the coffee, two spoons of sugar, and a dash of cream and milk, just how she liked it. She smiled behind her cup. It seemed the boy was buttering her up. "And that would be?"

"Mearing, this is going to completely ruin the way NEST sees you, but frankly, I need you to ban me from base."

She felt the blood drain from her face. Oh. Not Good.

~*~

TBC


	9. A Study in Tardis Blue

**Title:** Cause and Effect

**Disclaimer:** I neither own Doctor Who nor Transformers. Both belong to all respective creators, producers, and distributors. I make no money from this work of fiction.

**Rating:** PG-13

**Characters:** Sam, Captain Graham, Carly, 11th Doctor

**Summary:** Someone has been playing with History and Causality, and that is a Very. Not. Good. Thing…

**Note:** An in-depth discussion that led into this chapter is on my live journal. But here's where the origin of the idea came from: I was in Jury Duty, the selection panel just closed, and to break the ice, someone asked about a series of fictional works falling out of existence and the Universe bringing it to life to preserve Causality. This plot bunny seriously would NOT leave me alone! _Hopefully minor crossover with BBC's Sherlock._

Chapter 8: A Study in Tardis Blue (Part 1)

Sam knows something is wrong when Carly bounds into the Console Room, a heavy, leather-bound Tome in her hands.

"Doctor?" she called, pausing near the console, from under which, only Sam's legs were visible.

"Yes?" Sam asked.

"I found this book in the library..."

"And?"

"Well, it says it's written by Sir Arthur Conan Doyle..."

"Yes, yes, go on," Sam encouraged from under the Console, wondering if she'd found one of the early drafts of ACD's work in the library.

"Umm... It says it was written by Sir Arthur Conan Doyle..." Carly started again, but stopped.

"Spit it out, Carly," Sam said in a good natured tone, "Spare us all the suspense."

"Doctor! I'm holding a book that claims to have been written by Sir Arthur Conan Doyle, but Sir Arthur Conan Doyle never wrote the Adventures of Sherlock Holmes!"

"What?" Sam lurched out from under the console so quickly, his head banged against the edge. "Ack!" He rubbed his aching forehead with one hand and held out the other for the book, "Give it here, Carly."

She placed the book in his hand and watched apprehensively as he opened the book, flipping randomly through the pages, pale eyes rapidly scanning the text. Moments later, he closed the book and blew out a breath of air.

"Well," he murmured, "Everything seems to be in order."

"Doctor," Carly said warningly, "If this is a joke..."

"It's not," Sam cut her off firmly, "Something has gone terribly wrong, and this book," he hefted the tome in question, "is the remnant of a memory of an object that has been forgotten."

"Is that bad?" Carly asked, loosing some of her irritation.

"Yes," was all Sam said.

"Any idea what caused it?"

"Yes," Sam stood up and started pacing around the console platform, "Well, two ideas."

"And?"

"I think you should tell Captain Graham that we'll have an early start in the morning, and then go get some sleep. I need more data, which means we need to make another trip to London. Multiple trips. Starting with January 28, 2010. To St. Bartholomew's Hospital. We'll finish in 2009, in Dartmoor."

"So we're going backward chronologically?"

"No," Sam gently placed the book on a jumpseat and moved to fiddle with the controls, "We're moving forward chronologically across two years beginning in 2010 and then we're going to jump backwards, and quietly retrace my mission in Dartmoor in the area of June 15, 2009."

"What's in Dartmoor?"

"Baskerville Military Base," Graham said as he appeared in the leftmost entrance from the inner Tardis, "Why are we going back? You spent thirty six hours complaining about it not too long ago."

"Captain Graham," There was a hint of a soldier in Sam's tone, enough to bring the soldier in Graham screeching to attention, "you do recall my response to the Commanders at UNIT when I first received the dossier concerning the Dartmoor case? When I said something along the lines of _'This is not an episode of a highly popular television serial that won't be aired for another two years,'_?"

"Yessir, I remember, sir."

"Carly has brought a situation to my attention that would render that statement to have been made in error," Sam's eyes narrowed dangerously, "It also means that this is a Very. Not. Good. Thing."

Captain Thomas Graham, career soldier and commissioned officer, Chosen Companion of the Doctor, and Assistant to NEST's Civilian Liaison, gulped at the dangerous look in the young man's eyes. Suddenly he was reminded that although the Doctor outwardly looked human, he was actually an alien who was older than human civilization itself, one who had seen terrors and atrocities innumerable and had fought in a war which spanned all space and time, which his people both won and lost, leaving him the last of his kind. This youth, seemingly so charming most of the time, was no human youth on the cusp of manhood, but an ancient being who had seen much more than any human mind could imagine. He'd forgotten that it was not merely Samuel Witwicky he was traveling with, but also, the Doctor.

~*~

"Make visits. Go Shopping. Have fun. Do whatever," Sam said briskly as he pulled on his leather coat and strode to the Tardis doors, Graham close behind him, "Take the Tube, take the bus, and STAY. Out. Of. The. Cabs. And for goodness sake, Carly Spencer, stay out of trouble. Call if you need anything. Graham and I will be at St. Bartholomew's Hospital, either one of the labs or in the morgue."

~*~

Moments later, Sam was striding down the paths of a park. Graham found himself all but running to keep up with the young man.

"Why are we here, sir?" he asked cautiously, "I thought we were going to St Bartholomew's Hospital?"

"In a moment," Sam replied, "There is something I have to be sure of first."

"And that is?"

"John! John Watson!" a man called from a park bench.

The limping man in front of them paused and turned around, smiling wanly at the bespectacled man who had just risen from the park bench.

"Hmm..." Sam hummed thoughtfully, and lengthened his stride to carry him past the two men. Graham, as he had since Egypt, followed the youth obediently.

~*~

"St. Bartholomew's Hospital," Sam said dryly as he strode through it, "I had made plans to attend Cambridge next year, and maybe start training in here."

"HAve your plans changed then, sir?" Graham asked.

"That depends entirely on how this investigation turns out," Sam replied. He came to a stop and smiled, "Ah, here we are. The morgue."

He pushed open the door as a mousey haired woman said, "Oh! I'm terribly sorry, but you can't be here-"

Sam flashed his U.N.I.T. ID, "James Witwicky with UNIT." He gestured over his shoulder briefly, "This is Captain Graham with NEST. We're here about Shannon Opalson and Andrew McDonnell." He paused and said wryly, "We left a message."

"Oh!" she cried again, "I'm Molly Hooper, I'm terribly sorry, I didn't seem to have gotten the message! Also the surgery is currently in use. A detective is conducting an experiment about the lividity of bruising after death for a case..."

"It hardly matters," Sam interrupted, "Two people are dead and there are signs that this is only the start. It is imperative that we see the bodies, Dr. Hooper. At once."

"Ah... Alright."

Graham frowned as the woman caved completely under Sam's none too subtle barrage. This was not normal, was it? At least for this particular incarnation?

The morgue doors swung open and a man clad in a tailored suit with a blue scarf wrapped around his neck strode out, pulling on an old fashioned frock coat as he went.

"I need to get to the Lab, Molly, I'll be back to check the development of the bruises later!" he called as he swept past the group assembled at the door.

Graham glanced at Sam and felt his stomach drop to his feet. There was a forbidding expression on the youth's face, one that threatened a storm and warned people to tread carefully. Whatever it was that Sam had dragged them here to confirm had been confirmed, and the Boy was Not Happy.

~*~

They crashed into the Tardis, startling Carly, who was sorting several bags of new clothes into a five piece luggage set.

"Please don't tell me you used Tardis funds in a frivolous manner," Sam sighed, "If we spend everything at once, there's no Time Lord Way House for us to replaced used funds, you know."

"I ran into Doctor Jones who arranged for me to have access to your accounts," Carly said sheepishly, "The ones that you've had since the 70's."

Sam gave her a blank stare. "Well don't spend it all. I'm still paying off the Ponds' house and car. And we might need the funds later."

~*~

TBC


	10. Miracle Day

**Title:** Cause and Effect

**Disclaimer:** I neither own Doctor Who nor Transformers. Both belong to all respective creators, producers, and distributors. I make no money from this work of fiction.

**Rating:** PG-13

**Characters:** Sam, Ironhide, Ratchet, 11th Doctor, Captain Jack Harkness

**Summary:** The Doctor may be fire and rage and completely mad and wonderful, but he also does deliveries!

**Note:**Ok, don't get fooled by the title. This chapter has nothing to do with the Torchwood episode/arc of the same name.

Chapter 9: Miracle Day

Ironhide's holoform paces the small office irritably. It's been almost two months since a ship with a larger interior than its exterior materialized around him, saving him from the brunt of Sentinel Prime's Cosmic Rust Cannon, only to dematerialize, leaving behind a rusted frame that bore a striking resemblance to Ironhide himself. The weapons specialist then learned the reason for the sudden turn around in the British portion of NEST's opinion of Sam. found himself dropped off at a location that Samuel claimed was Roald Dahl Plass. Jack Harkness steps into the front office from the back, carrying a book, and he glanced at the pacing figure briefly.

"Pacing isn't going to bring the Doctor here any sooner, you know," he said cautiously. "You were brought here for a reason, Ironhide. He'll come back for you when time comes. He always comes back eventually."

"Define eventually," Ironhide grumbled, "Because from what I hear, his sense of timing is atrocious."

"Don't worry, Ironhide," Jack said gently, "Even if he's late, the Doctor is a Time Lord, remember? As far as NEST will be concerned, you won't have been gone for very long."

"But I will have been gone for however long I am stuck here."

"Sad but true," Jack shrugged, "Look at it this way, you are now officially a Companion to the Doctor. You have access to resources that were previously closed to you."

"Except perhaps the ones available to my own kind," Ironhide grumbled.

"Oh, you'll be surprised," Jack mused, "When it comes to his Companions, the Doctor never fails to provide. He simply doesn't hand us everything on a silver platter, that's all."

"I'm not his companion," Ironhide said dryly, "Sam has Carly and Captain Graham."

"Not all of the Doctor's Companions ever leave Earth or are traveling Companions," Jack said pointedly, "Look at Wilfred Mott, Jo Grant, the late General Alistair Gordon Lethbridge-Stewart, Captain Yates and Sergeant Benton. They're considered Companions because the Doctor treasured them as friends. He went out of his way to save your life, Ironhide, that means that you count for something."

Ironhide didn't look convinced, "Then why would he separate himself from us?"

"For the same reason why he never comes back after we leave him," Jack said softly, "Because sometimes, we have to stand on our own two feet, and we can't do that if we're too busy hero worshipping him. He separates himself from us because he cares."

"Nice to know someone appreciates my effort," a man's voice said wryly from thin air.

"Hey, Doctor! I didn't know the Tardis had a stealth mode," Jack called.

The Tardis shimmered into view and the door swung open. A lanky man dressed in a green wool overcoat and red bow tie all but bounced out of the Tardis and said wryly, "All ships have a cloaking function. We simply do not often encounter situations where the Tardis is required to enter stealth mode. Now, Ironhide, was it? Time to get back to your main body, places to go, people to see! I was told that since the Battle Protocols have gone dormant, your mate is beginning to notice that his bond with you is still active. I'm to take you the short way round rather than leaving you to wait ten years. Jack, I'll see you in my future."

"Where is Sam?" Ironhide asked the strange man, who, based on Jack Harkness's reaction, was the Doctor. Possibly a former version.

The Doctor blinked, "Sam? Who? Ah, you mean future me. He's dashing about out there somewhere with that girl, what was her name again? Carla? Cathy? Kitty? Ah, never mind, I'll find out eventually. Let's get you home, shall we?" He spun around and vanished back inside the Tardis, which dematerialized with a groan and a wheeze.

~*~

"He's still alive, I know it!"

"Ratchet," First Aid said tiredly, "Ironhide is gone. We have his empty frame to prove it."

"I still have the bond!"

"Spark echoes," the younger medic sighed. It was an argument that they'd had multiple times since Sam and Carly vanished after Chicago, when in the end of battle, when the Battle and Emergency Protocols had gone dormant once they were no longer needed, because once things had settled down, that was when Ratchet found anomalous readings in his spark. Or so the Medic thought, because First Aid had scanned his mentor multiple times, and not once did any readings come up to prove any of Ratchet's claim of possible Spark damage. Then again, the Spark damage caused by a broken Pair Bond was, despite eons of study, something that the medical field could only hope to scratch the surface of.

Suddenly, there was a loud clanking and wheezing noise that characterized the fabric of the universe being twisted, and a small blue box appeared in the middle of the hanger. The door swung open and a the torso of a man with floppy brown hair and green eyes clad in a green wool overcoat with a red bow tie leaned out and said, "Special Delivery to the Autobots of Diego Garcia from the Doctor, courtesy of Sam Witwicky!" He vanished back into the box, and the doors slammed shut. With a groan and a wheeze, the box slowly dematerialized, leaving behind a shiny black GMC Topkick, which immediately whirred to life, parts shifting and moving to reveal Ironhide, whole and healthy.

"Wha-?" Was the general consensus around the hanger, with the exception of Ratchet who immediately launched himself at his bonded with a shout.

Meanwhile, Nine Hundred Sixty Eight trillion Lightyears away, Sam Witwicky opened his eyes in his bedroom on the Tardis and smiled.

~*~

TBC


	11. Homemaking

**Title:** Cause and Effect

**Disclaimer:** I neither own Doctor Who nor Transformers. Both belong to all respective creators, producers, and distributors. I make no money from this work of fiction.

**Rating:** PG-13

**Characters:** Sam, Sam, Captain Graham, 11th Doctor, Jack Harkness, Martha Jones, Mickey Smith, Amy and Rory Pond, River Song

**Summary:** Sometimes Sam wonders if it is a good idea to let any of the Doctor's former companions to meet.

Chapter 8: Homemaking

The truth is, UNIT would take Samuel Witwicky into their fold, with or without an education from high-end colleges, as would NEST. If in fact, Sam ever chose, he could probably go to Torchwood and get a job there if he could ever stop associating Torchwood with the loss of the one person who had made the universe beautiful again and showed him that life was worth living. Truth be told, Sam could very likely travel to anyplace in the universe and be assured of some occupation in one form or another. Which is why former Companions Jack Harkness, Martha Jones, Mickey Smith, and Amy and Rory Pond, were so surprised when Sam popped up in London, Tardis and current Companion, Carly Spencer in tow, and declared that he would be attending college in Cambridge, and would later study medicine in St. Bartholomew's Hospital.

"But you have the Tardis!" Martha protested even as she helped Sam carry a box out of his bright yellow Camaro and into his new flat, where he was directing Mickey and Jack and several NEST soldiers who were unloading furniture from the trailer hitched to a semi painted with blue and red ghost flames. "Why would you rent a flat and live in it while the Tardis is in the back room? In fact, why are you even doing this? You're smarter than every human on this planet combined!"

"It would look quite strange if someone were to come over and the only bit of furniture I had was a blue police box, yes? Best to blend in, Martha."

"Ok, good point, but why are you even studying medicine here? In the twenty first century? You know more about medicine than any of us!"

"I can render emergency care to upward toward thirty thousand different species, Martha," Sam sighed, "But just because I know a wide range of emergency medical techniques doesn't mean there isn't always more to learn. As for why twenty-first century medicine when I could be studying fifty-first century medicine... There is something going on in Twenty-first Century London I want to keep an eye on, and the easiest way to to undergo medical training in St. Bartholomew's Hospital. Those two idiots practically make the morgue and the labs their second home. Well, third home. They spend more time in New Scotland Yard."

"If they spend so much time in Scotland Yard, Doctor," Mickey said, "Wouldn't it be better to be doing law enforcement training?"

"Oh, yes, put myself in a position where I would be under the eye of the cleverest most observant human alive for a long period of time, yes, very clever, Mickey. Sherlock would immediately know that I was watching him, and even if he, by some miracle didn't notice me watching him, his soldier friend certainly would." Sam shook his head, "In my current circumstances, since I'm technically traceable, unlike previously, I'd end up with a visit from the British Government, and frankly, the universe hangs in the balance and I have neither the time nor inclination to participate in a pissing contest with That Man."

"What man?" Carly asked, carrying a box labeled Fragile Glassware, into the kitchen.

"I won't say his name," Sam said, shaking his head, "As we never know who is listening. But he is tremendously clever, one of the cleverest people alive."

"Oh, come off it, Doctor," Mickey laughed as he wheeled a mini-fridge into the flat, "No one is that clever."

"Oi!" Sam cried, "I iam/i that clever!"

"Yes, but you're an alien," Rory said dryly, "Where do you want these?" He hefted the bags of shopping slightly.

"Okay. Point," Sam agreed, "and Mickey can tuck the mini-fridge into a spare corner of the kitchen," Sam directed, "and really, Rory, the shopping goes into the fridge, obviously." He makes a face that he knows is as close to the crinkly, mock annoyed expression that his eleventh form used to wear as his current face can get.

"Your face isn't expressive enough for that goofy look anymore, Raggedy Man," Amy laughs as she hauls in several more bags of shopping.

"Goodness!" Sam said cheerfully, "How much did the pair of you get? I'm only one person, Ponds! I can't possibly eat that much!"

"It's not all food, Sweetie," River swooped in and plunked a square bamboo coaster onto the mantle and stacked a powder blue candle in a glass jar on top of the coaster, "There are things to make this house a home."

"I could just as easily have the Tardis synthesize what I need," Sam protested.

"True," River admitted, "But if something happens and for whatever reason, those people come in here, do you really want them to notice that not everything in this house is period appropriate?"

"I am supposedly a twenty year old American Male, who has finished training in forensic science with a degree in organic chemistry, microbiology, sociology, anthropology, computer engineering, physics, astrophysics, linguistics and history, and is currently in London to finish up medical training. I am quite sure any oddities will be put down as my being an eccentric genius."

"With normal people, yes," Jack strides in carrying a round oak table, "But you're no ordinary person, now are you? And from what you've told me, these men you're investigating are no ordinary people either."

"When did the lot of you get so clever?" Sam asked in mock confusion, "And if you were all so clever, then why did you never put that cleverness to use when you were travelling in the Tardis?"

"Twenty-fisrt century Human," Martha put her hand in the air.

"Us too," Carly, Mickey, Amy, and Rory chimed in.

"Fifty First century human," Jack called, "and still not as clever as you are."

"Criminal in Stormcage, Sweetie," River chuckled.

"And you walk in and out of Stormcage like the walls aren't even there," Sam replied.

"Please," River scoffed, "As if any place could hold me or you against our will." She paused and added, "Except maybe the Tardis."

"Well, yes," Sam agreed. "So, housewarming party, anyone?"

"Uh, Doctor, that comes after you've moved in," Amy said.

"And I am moved in!" Sam protested.

"Moved in as in nothing left to unpack, Sir," Graham said as he and a random soldier carried in a wingbacked reclining chair.

"Drat you all..."

~*~

TBC


	12. The Mind and the Heart

**Title:** Cause and Effect**  
>Disclaimer:<strong> I neither own Doctor Who nor Transformers. Both belong to all respective creators, producers, and distributors. I make no money from this work of fiction.  
><strong>Rating:<strong> PG-13  
><strong>Characters:<strong> Sam, 11th Doctor, Sherlock Holmes, John Watson  
><strong>Summary:<strong> Sometimes the Doctor meets his Companions out of order. Sam is decidedly not pleased when this happens.  
><strong><span>Important Note:<span>** Because Time is not a linear progression and is instead a big ball of wibbly-wobbly, timey-whimey... Stuff.

Chapter 12: The Mind and the Heart

Sam shut the door of 209C with more force than was necessary and tossed a bag onto the coffee table and in the same motion, flopped down onto the sofa with a groan. He slung an arm over his eyes and sighed. It really didn't matter how much of a genius he was, in the medical field, it was simply not done to test out, no matter how tedious a class was. As a result, Sam, who had gotten used to the fast track life of the Tardis and testing in and out of classes in Princeton and Cambridge, found himself bored out of his skull traversing his training the long way at St. Bartholomew's Hospital. Funnily enough, boredom was more exhausting than running down successive stretches of corridors for one's life. Still, if it hadn't meant that his peers in St. Bartholomew's would have given him evil looks and that he'd likely find it rather difficult to find work in the future, Sam would have gladly tested out of several classes the way he had in Princeton and Cambridge. Still, he hated the slow route. Give him adventures and adrenaline any day. Anything as long as it was not this mind numbing stretch of boredom.

A quiet click drifts up the stairs. There is gentle grinding noise, lower than the human ear can hear. Sam turns his head so his right ear is aimed at the door. He hears the tmptmptmptmp of quiet footfalls. Based on the patterns and the differences in impact, two people, the timing between each footfall showed that one was taller than the other and one weighed less than the other. The unconscious psychic emanations that Sam could just barely feel because of his half-breed status indicated excitement and vague annoyance and exasperation, but no malice. Whomever was coming had no ill intent, the only problem being that they were heading straight down the stairs for the basement flat and the two were strangers.

"Walk quieter, John!" a low baritone hissed, "He'll know we're here!"

"If the Doctor's in, then he already knows we're here, Sherlock," a different voice murmured, a vague hint of exasperated affection slipping into his voice.

Sam felt a pang of annoyance. Another case of people knowing him before he knew them then. Lovely. He'd never liked such situations, after all, look at what happened with Mel and River. Or better yet, look at what occurred because of Mel and River, see how he'd always second guessed himself when dealing with the two, worried that he might upset the timeline with a misstep. Thank goodness that such encounters were rare, even with the multiple different versions of himself floating around the universe at any given time.

There was a soft clattering from the door, the sound of a lock being picked. Sam made the snap decision to nip the situation in the bud.

"Whomever you are, leave that lock alone and go away!"

"Don't be silly, Doctor," the baritone replied, "Let us in."

"Not by the hair on my chinny chin chin!"

There was a pause and the owner of the baritone said in a confused tone, "Was that supposed to be a no?" while the other voice sniggered.

"That's a rather vehement, 'No,' Sherlock."

"Well, why didn't he just say so?"

"When, in all of time and space, has the Doctor ever given us a straight answer?"

"Good point. Still, we're coming in, Doctor!"

"Rassilon forbid that I ever have Companions who do as they are told," Sam muttered and closed his eyes as the lock clicked and the door swung open.

"If we were prone to doing as we were told, we would be boring, and you would never have taken us onto the Tardis," The owner of the Baritone announced as he flounced into the room, swishing his coat dramatically. The other man followed more sedately after closing the door behind them.

"You look like you had a long day, Doctor," he remarked.

"Why are you in London anyway?" Sherlock demanded, "You're normally rushing about in the Tardis, and here you are taking the long way."

"I've taken the long route before you know," Sam murmured, "Most of the time, my life does not involve running down corridors or city streets being shot at."

"But it's much more interesting!" Sherlock protested.

"Nope. Nothing doing. Future Companions, out!"

"Oh," Sherlock paused, "You haven't met us yet."

"And now I have. Out please."

Like all other Companions he'd ever had, they ignore him when he orders them, but when he asks nicely, they obey. The two leave.

"Um…" the other voice said cautiously, "I'll leave our numbers and address here. Call us or drop by when you feel better, Doctor."

There is the sound of a card being set on the table, heavy, uneven footsteps are muffled by the door clicking shut and the murmur of voices from the hall fade as they climb the stairs. Sam turns his head and cracks an eye open at the card propped up against his bag.

"Sherlock Holmes and Captain John H. Watson MD. Consulting Detectives."

Sam sat upright, starring incredulously at the card.

"What on Gallifrey?"

~*~

End


End file.
